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PloS One Feb 2011Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased... (Comparative Study)
Comparative Study
Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca.
Topics: Adult; Aged; Blood Chemical Analysis; Blood Proteins; Case-Control Studies; Databases, Protein; Female; Gas Chromatography-Mass Spectrometry; Health; Humans; Lipids; Male; Metabolome; Metabolomics; Middle Aged; Nuclear Magnetic Resonance, Biomolecular; Osmolar Concentration; Review Literature as Topic; Serum; Spectrometry, Mass, Electrospray Ionization
PubMed: 21359215
DOI: 10.1371/journal.pone.0016957 -
Scandinavian Journal of Immunology Mar 2022Why should we explore and study disease mechanisms? This is particularly important when we are dealing with complex pathogenesis without a direct causal agent, for... (Review)
Review
Why should we explore and study disease mechanisms? This is particularly important when we are dealing with complex pathogenesis without a direct causal agent, for example, syndromes with multiple organ involvements. Sjögren's syndrome is definitely such an entity. Also, there are a number of reasons for such studies such as disclosing the aetiology, to identify biomarkers for diagnosis and assessment of the disease process and monitor response to treatment, to determine targets for treatment, to define critical items in classification criteria, amongst others. Samples available for the study of disease mechanisms in Sjögren's syndrome have included serum (autoantibodies, cytokines), DNA (gene profiling, GWAS), cells (phenotypes/flow cytometry, proportion of cells/CyTOF), tissue (focal inflammation, germinal centres, mass cytometry), and saliva (proteomics, biochemistry, mucosal immunity). An original explanatory concept for the pathogenesis of Sjögren's syndrome proposed a specific and self-perpetuating immune-mediated loss of exocrine tissue as the principal cause of glandular hypofunction. This hypothesis however falls short of accommodating several Sjögren's syndrome-related phenomena and experimental findings. Today, the emergence of advanced bio-analytical platforms has further enabled the identification of central pathogenic processes and potential biomarkers. The purpose of this minor review is to highlight a selection of previous but also recent and novel aspects on the disease mechanisms in Sjögren's syndrome.
Topics: Animals; Biomarkers; Humans; Saliva; Serum; Sjogren's Syndrome
PubMed: 35073430
DOI: 10.1111/sji.13145 -
Journal of Visualized Experiments : JoVE Mar 2017Monolayer cell culture does not adequately model the in vivo behavior of tissues, which involves complex cell-cell and cell-matrix interactions. Three-dimensional (3D)...
Monolayer cell culture does not adequately model the in vivo behavior of tissues, which involves complex cell-cell and cell-matrix interactions. Three-dimensional (3D) cell culture techniques are a recent innovation developed to address the shortcomings of adherent cell culture. While several techniques for generating tissue analogues in vitro have been developed, these methods are frequently complex, expensive to establish, require specialized equipment, and are generally limited by compatibility with only certain cell types. Here, we describe a rapid and flexible protocol for aggregating cells into multicellular 3D spheroids of consistent size that is compatible with growth of a variety of tumor and normal cell lines. We utilize varying concentrations of serum and methyl cellulose (MC) to promote anchorage-independent spheroid generation and prevent the formation of cell monolayers in a highly reproducible manner. Optimal conditions for individual cell lines can be achieved by adjusting MC or serum concentrations in the spheroid formation medium. The 3D spheroids generated can be collected for use in a wide range of applications, including cell signaling or gene expression studies, candidate drug screening, or in the study of cellular processes such as tumor cell invasion and migration. The protocol is also readily adapted to generate clonal spheroids from single cells, and can be adapted to assess anchorage-independent growth and anoikis-resistance. Overall, our protocol provides an easily modifiable method for generating and utilizing 3D cell spheroids in order to recapitulate the 3D microenvironment of tissues and model the in vivo growth of normal and tumor cells.
Topics: Cell Aggregation; Cell Culture Techniques; Cell Line, Tumor; Humans; Methylcellulose; Serum; Spheroids, Cellular; Time Factors
PubMed: 28448014
DOI: 10.3791/55544 -
ACS Chemical Biology Jun 2022Fluorescent Zn sensors play a pivotal role in zinc biology, but their application in complex media such as blood serum or plate reader-based cellular assays is hampered...
Fluorescent Zn sensors play a pivotal role in zinc biology, but their application in complex media such as blood serum or plate reader-based cellular assays is hampered by autofluorescence and light scattering. Bioluminescent sensor proteins provide an attractive alternative to fluorescent sensors for these applications, but the only bioluminescent sensor protein developed so far, BLZinCh, has a limited sensor response and a suboptimal Zn affinity. In this work, we expanded the toolbox of bioluminescent Zn sensors by developing two new sensor families that show a large change in the emission ratio and cover a range of physiologically relevant Zn affinities. The LuZi platform relies on competitive complementation of split NanoLuc luciferase and displays a robust, 2-fold change in red-to-blue emission, allowing quantification of free Zn between 2 pM and 1 nM. The second platform was developed by replacing the long flexible GGS linker in the original BLZinCh sensor by rigid polyproline linkers, yielding a series of BLZinCh-Pro sensors with a 3-4-fold improved ratiometric response and physiologically relevant Zn affinities between 0.5 and 1 nM. Both the LuZi and BLZinCh-Pro sensors allowed the direct determination of low nM concentrations of free Zn in serum, providing an attractive alternative to more laborious and/or indirect approaches to measure serum zinc levels. Furthermore, the genetic encoding of the BLZinCh-Pro sensors allowed their use as intracellular sensors, where the sensor occupancy of 40-50% makes them ideally suited to monitor both increases and decreases in intracellular free Zn concentration in simple, plate reader-based measurements, without the need for fluorescence microscopy.
Topics: Fluorescent Dyes; Humans; Luciferases; Luminescent Proteins; Serum; Zinc
PubMed: 35611686
DOI: 10.1021/acschembio.2c00227 -
Journal of Proteome Research Apr 2022Blood derivatives are the biofluids of choice for metabolomic clinical studies since blood can be collected with low invasiveness and is rich in biological information....
Blood derivatives are the biofluids of choice for metabolomic clinical studies since blood can be collected with low invasiveness and is rich in biological information. However, the choice of the blood collection tubes has an undeniable impact on the plasma and serum metabolic content. Here, we compared the metabolomic and lipoprotein profiles of blood samples collected at the same time and place from six healthy volunteers but using different collection tubes (each enrolled volunteer provided multiple blood samples at a distance of a few weeks/months): citrate plasma, EDTA plasma, and serum tubes. All samples were analyzed via nuclear magnetic resonance spectroscopy. Several metabolites showed statistically significant alterations among the three blood matrices, and also metabolites' correlations were shown to be affected. The effects of blood collection tubes on the lipoproteins' profiles are relevant too, but less marked. Overcoming the issue associated with different blood collection tubes is pivotal to scale metabolomics and lipoprotein analysis at the level of epidemiological studies based on samples from multicenter cohorts. We propose a statistical solution, based on regression, that is shown to be efficient in reducing the alterations induced by the different collection tubes for both the metabolomic and lipoprotein profiles.
Topics: Blood Specimen Collection; Citric Acid; Humans; Metabolomics; Plasma; Serum
PubMed: 35271285
DOI: 10.1021/acs.jproteome.1c00935 -
Scientific Reports Apr 2019In the research field of extracellular vesicles (EVs), the use of fetal bovine serum (FBS) depleted of EVs for in vitro studies is advocated to eliminate the confounding...
In the research field of extracellular vesicles (EVs), the use of fetal bovine serum (FBS) depleted of EVs for in vitro studies is advocated to eliminate the confounding effects of media derived EVs. EV-depleted FBS may either be prepared by ultracentrifugation or purchased commercially. Nevertheless, these preparations do not guarantee an RNA-free FBS for in vitro use. In this study we address the RNA contamination issue, of small non-coding (nc)RNA in vesicular or non-vesicular fractions of FBS, ultracentrifugation EV-depleted FBS, commercial EV-depleted FBS, and in our recently developed filtration based EV-depleted FBS. Commercially available serum- and xeno-free defined media were also screened for small ncRNA contamination. Our small ncRNA sequencing data showed that all EV-depleted media and commercially available defined media contained small ncRNA contaminants. Out of the different FBS preparations studied, our ultrafiltration-based method for EV depletion performed the best in depleting miRNAs. Certain miRNAs such miR-122 and miR-203a proved difficult to remove completely and were found in all media. Compared to miRNAs, other small ncRNA (snRNA, Y RNA, snoRNA, and piRNA) were difficult to eliminate from all the studied media. Additionally, our tested defined media contained miRNAs and other small ncRNAs, albeit at a much lower level than in serum preparations. Our study showed that no media is free of small ncRNA contaminants. Therefore, in order to screen for baseline RNA contamination in culturing media, RNA sequencing data should be carefully controlled by adding a media sample as a control. This should be a mandatory step before performing cell culture experiments in order to eliminate the confounding effects of media.
Topics: Animals; Cattle; Culture Media, Serum-Free; Extracellular Vesicles; Humans; MicroRNAs; Sequence Analysis, RNA; Serum
PubMed: 30940830
DOI: 10.1038/s41598-019-41772-3 -
International Journal of Environmental... Oct 2023Some types of per- and poly-fluoroalkyl substances (PFAS) have been banned over the last two decades, but millions of Americans continue to have exposure to the...
Some types of per- and poly-fluoroalkyl substances (PFAS) have been banned over the last two decades, but millions of Americans continue to have exposure to the compounds through drinking water and consumer products. Therefore, understanding the changes in serum PFAS concentrations after their limited use is necessary to protect public health. In this study, we evaluated trends of serum PFAS compounds (PFOS, PFOA, PFHxS, PFDA, and PFNA) to determine their distribution among the United States general population. We analyzed serum concentrations of PFAS measured from random subsamples of the National Health and Nutrition Examination Survey (NHANES) participants. The study results demonstrated that demographic factors such as race/ethnicity, age, and sex may influence the levels of serum PFAS over time. Adults, males, Asians, Non-Hispanic Blacks, and Non-Hispanic Whites had high risks of exposure to the selected PFAS. Overall, serum PFAS levels declined continuously in the studied population from 1999 to 2018. Among the studied population, PFOS and PFDA were the most and least prevalent PFAS in blood serum, respectively. Serum levels of PFDA, PFOA, and PFHxS showed upward trends in at least one racial/ethnic group after 2016, which underscores the need for continuous biomonitoring of PFAS levels in humans and the environment.
Topics: Male; Humans; Adult; Adolescent; United States; Nutrition Surveys; Environmental Pollutants; Alkanesulfonic Acids; Serum; Caprylates; Fluorocarbons
PubMed: 37947542
DOI: 10.3390/ijerph20216984 -
Scientific Reports Jul 2022The majority of metabolomics studies to date have utilised blood serum or plasma, biofluids that do not necessarily address the full range of patient pathologies. Here,...
The majority of metabolomics studies to date have utilised blood serum or plasma, biofluids that do not necessarily address the full range of patient pathologies. Here, correlations between serum metabolites, salivary metabolites and sebum lipids are studied for the first time. 83 COVID-19 positive and negative hospitalised participants provided blood serum alongside saliva and sebum samples for analysis by liquid chromatography mass spectrometry. Widespread alterations to serum-sebum lipid relationships were observed in COVID-19 positive participants versus negative controls. There was also a marked correlation between sebum lipids and the immunostimulatory hormone dehydroepiandrosterone sulphate in the COVID-19 positive cohort. The biofluids analysed herein were also compared in terms of their ability to differentiate COVID-19 positive participants from controls; serum performed best by multivariate analysis (sensitivity and specificity of 0.97), with the dominant changes in triglyceride and bile acid levels, concordant with other studies identifying dyslipidemia as a hallmark of COVID-19 infection. Sebum performed well (sensitivity 0.92; specificity 0.84), with saliva performing worst (sensitivity 0.78; specificity 0.83). These findings show that alterations to skin lipid profiles coincide with dyslipidaemia in serum. The work also signposts the potential for integrated biofluid analyses to provide insight into the whole-body atlas of pathophysiological conditions.
Topics: COVID-19; Humans; Lipids; Metabolomics; Saliva; Sebum; Serum
PubMed: 35831456
DOI: 10.1038/s41598-022-16123-4 -
Stem Cell Research & Therapy May 2018Canine MuStem cells have demonstrated regenerative efficacy in a dog model of muscular dystrophy, and the recent characterization of human counterparts (hMuStem) has...
BACKGROUND
Canine MuStem cells have demonstrated regenerative efficacy in a dog model of muscular dystrophy, and the recent characterization of human counterparts (hMuStem) has highlighted the therapeutic potential of this muscle-derived stem cell population. To date, these cells have only been generated in research-grade conditions. However, evaluation of the clinical efficacy of any such therapy will require the production of hMuStem cells in compliance with good manufacturing practices (GMPs). Because the current use of fetal bovine serum (FBS) to isolate and expand hMuStem cells raises several ethical, safety, and supply concerns, we assessed the use of two alternative xeno-free blood derivatives: human serum (HS) and a human platelet lysate (hPL).
METHODS
hMuStem cells were isolated and expanded in vitro in either HS-supplemented or hPL-supplemented media and the proliferation rate, clonogenicity, myogenic commitment potential, and oligopotency compared with that observed in FBS-supplemented medium. Flow cytometry and high-throughput 3'-digital gene expression RNA sequencing were used to characterize the phenotype and global gene expression pattern of hMuStem cells cultured with HS or hPL.
RESULTS
HS-supplemented and hPL-supplemented media both supported the isolation and long-term proliferation of hMuStem cells. Compared with FBS-based medium, both supplements enhanced clonogenicity and allowed for a reduction in growth factor supplementation. Neither supplement altered the cell lineage pattern of hMuStem cells. In vitro differentiation assays revealed a decrease in myogenic commitment and in the fusion ability of hMuStem cells when cultured with hPL. In return, this reduction of myogenic potential in hPL-supplemented cultures was rapidly reversed by substitution of hPL with HS or fibrinogen-depleted hPL. Moreover, culture of hMuStem cells in hPL hydrogel and fibrinogen-depleted hPL demonstrated that myogenic differentiation potential is maintained in heparin-free hPL derivatives.
CONCLUSIONS
Our findings indicate that HS and hPL are efficient and viable alternatives to FBS for the preparation of hMuStem cell batches in compliance with GMPs.
Topics: Adolescent; Adult; Animals; Blood Platelets; Cell Differentiation; Cell Proliferation; Cell- and Tissue-Based Therapy; Dogs; Female; Humans; Male; Serum; Young Adult
PubMed: 29720259
DOI: 10.1186/s13287-018-0852-y -
International Journal of Environmental... Jun 2022Background: Pesticides manage pests and diseases in agriculture, but they harm the health of agricultural workers. Concentrations of thirteen pesticides were determined...
Background: Pesticides manage pests and diseases in agriculture, but they harm the health of agricultural workers. Concentrations of thirteen pesticides were determined in personal air and blood serum of 85 paddy farmers and 85 non-farmers, thereafter associated with health symptoms. Method: Samples were analyzed using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Results: The median concentration of pesticides in personal air samples ranged from 10.69 to 188.49 ng/m3 for farmers and from 5.79 to 73.66 ng/m3 for non-farmers. The median concentration of pesticides in blood serum was from 58.27 to 210.12 ng/mL for farmers and 47.83 to 62.74 ng/mL for non-farmers. Concentration of eleven pesticides in personal air and twelve pesticides in blood serum were significantly higher in farmers than non-farmers (p < 0.05). All pesticides detected in personal air correlated significantly with concentration in the blood serum of farmers (p < 0.05). Health symptoms reported by farmers were dizziness (49.4%), nausea (47.1%), cough (35.3%), chest pain (30.6%), breathing difficulty (23.5%), sore throat (22.4%), vomiting (18.8%), phlegm (16.5%), and wheezing (15.3%). Concentration of pesticides in personal air, blood serum, and health symptoms were not significantly associated. Conclusion: Occupational exposure to pesticides significantly contaminates blood serum of farmers compared to non-farmers.
Topics: Agriculture; Cross-Sectional Studies; Farmers; Humans; Malaysia; Occupational Exposure; Pesticides; Serum; Tandem Mass Spectrometry
PubMed: 35682390
DOI: 10.3390/ijerph19116806